Here we present CoVaCS, a fully automated, highly accurate system with a web based graphical interface for genotyping and variant annotation. Extensive tests on a gold standard benchmark data-set -the NA12878 Illumina platinum genome- confirm that call-sets based on our consensus strategy are completely in line with those attained by similar command line based approaches, and far more accurate than call-sets from any individual tool. Importantly our system exhibits better sensitivity and higher specificity than equivalent commercial software.
CoVaCS offers optimized pipelines integrating state of the art tools for variant calling and annotation for whole genome sequencing (WGS), whole-exome sequencing (WES) and target-gene sequencing (TGS) data. The system is currently hosted at Cineca, and offers the speed of a HPC computing facility, a crucial consideration when large numbers of samples must be analysed. Importantly, all the analyses are performed automatically allowing high reproducibility of the results. As such, we believe that CoVaCS can be a valuable tool for the analysis of human genome resequencing studies. CoVaCS is available at: https://bioinformatics.cineca.it/covacs .
这里我们介绍CoVaCS,一个完全自动化的,具有用于基因分型和变异注释的基于Web的图形界面的高精度系统。对黄金标准基准数据集(NA12878Illumina铂金基因组)的广泛测试证实,基于我们共识策略的调用集与基于类似命令行的方法获得的调用集完全一致。并且比任何单个工具的调用集更准确。重要的是,我们的系统比同等的商业软件具有更好的灵敏度和更高的特异性。
CoVaCS提供优化的管道,整合了用于全基因组测序(WGS)的变体调用和注释的最新工具,全外显子组测序(WES)和靶基因测序(TGS)数据。该系统目前托管在Cineca,并提供HPC计算设施的速度,当必须分析大量样品时,这是一个至关重要的考虑因素。重要的是,所有分析均自动进行,结果具有较高的重现性.因此,我们相信CoVaCS可以成为分析人类基因组重测序研究的有价值的工具.CoVaCS可在以下网址获得:https://生物信息学。Cineca.it/covacs。